I've done some more tinkering and I've fixed the problem myself. I've
included the solution below in case it's useful to anyone who comes across
this issue too.

I found that the pbc wrap command contains an animate command to rewind
back to the frame you started on. If you comment out the line containing
the animate command in pbcwrap.tcl in your VMD installation the problem is
fixed.

I.e. in Contents/vmd/plugins/noarch/tcl/pbctools2.8/pbcwrap.tcl put a '#'
in front of 'animate'

This of course removes the rewind functionality from your version of
pbctools. This is also a problem if you're using VMD on a machine where you
don't have permissions to modify any files associated with VMD. To fix both
of these issues I've implemented a -bigdcd flag into a local version of
pbctools which is loaded instead of the distributed version. You can find
the custom version at https://github.com/tmgriffiths/pbctools. The -bigdcd
flag for pbc wrap is identical to -now, but skips pbc wrap's internal
animate command.

To use your own customised version of a package you'll need to place a
version of the package somewhere on your system that you can access (I use
$HOME/bin/vmd) and add the following line to your .vmdrc file:

This command places $HOME/path/to/your/version at the beginning of
$auto_path ensuring your version of pbctools (or any other package) will be
found first and take preference over the distributed version.